Anisha Keshavan

and 3 more

OVERVIEW There is a disconnect between clinical disability in multiple sclerosis (MS) and structural damage seen on MRI, called the clinico-radiological paradox . Even though focal white matter lesions seen on MRI largely characterize multiple-sclerosis, lesion volumes are not strongly correlated with clinical motor disability . Possible reasons for this paradox include lesion location and gray matter atrophy , however the correlations with disability are modest (r=0.3). Another hypothesis is that functional adaptation plays a role, where brains adapt to the damage caused by MS in order to minimize disability. My preliminary results have shown that changes in functional MRI network connections correlate with performance on a complex motor dexterity task, even after accounting for structural damage. However, poor performance on a complex motor task may not be attributable to motor network damage and reorganization alone. For example, damage to the visual pathway involved in a complex task may confound results. Therefore, I propose to study how performance on simpler motor tasks relate to functional network connectivity changes, and develop a functional biomarker to predict motor performance. I intend to measure the central motor conduction time (CMCT), which is sensitive to corticospinal tract damage, by measuring motor evoked potentials (MEP) using transcranial magnetic stimulation (TMS). Additionally, finger tapping speed (FT) will be collected on MS patients, which has been shown to be more impaired in MS patients compared to measures of manual dexterity. Functional biomarkers will be developed using a traditional, hypothesis driven approach, followed by a functional dynamic network analysis focused on the posteriomedial cortex (PMC). Features of the functional network will be extracted based on CMCT and FT. This will result in a biomarker that reflects the ability of a subject to functionally adapt to MS-related damage to the motor system, which could lead to personalized medical treatment of their disease. Specific Aim 1: Develop an fMRI metric that relates to CMCT and FT using a hypothesis driven analysis Specific Aim 2: Improve on the prediction of simple and complex motor tasks by developing an fMRI metric based on dynamic functional connectivity of the PMC
Mindcontrol meteor diagram1

Anisha Keshavan

and 6 more

Tissue classification plays a crucial role in the investigation of normal neural development, brain-behavior relationships, and the disease mechanisms of many psychiatric and neurological illnesses. Ensuring the accuracy of tissue classification is important for quality research and, in particular, the translation of imaging biomarkers to clinical practice. Assessment with the human eye is vital to correct various errors inherent to all currently available segmentation algorithms. Manual quality assurance becomes methodologically difficult at a large scale - a problem of increasing importance as the number of data sets is on the rise. To make this process more efficient, we have developed Mindcontrol, an open-source web application for the collaborative quality control of neuroimaging processing outputs. The Mindcontrol platform consists of a dashboard to organize data, descriptive visualizations to explore the data, an imaging viewer, and an in-browser annotation and editing toolbox for data curation and quality control. Mindcontrol is flexible and can be configured for the outputs of any software package in any data organization structure. Example configurations for three large, open-source datasets are presented: the 1000 Functional Connectomes Project (FCP), the Consortium for Reliability and Reproducibility (CoRR), and the Autism Brain Imaging Data Exchange (ABIDE) Collection. These demo applications link descriptive quality control metrics, regional brain volumes, and thickness scalars to a 3D imaging viewer and editing module, resulting in an easy-to-implement quality control protocol that can be scaled for any size and complexity of study.

Anisha Keshavan

and 8 more

Rationale Advances in MRI technology and image segmentation algorithms have enabled researchers to begin to understand the mechanisms of healthy brain development and neurological disorders, such as multiple sclerosis . Due to the wide variability of brain morphology, coupled with a pathological process in the case of neurological disorders, increasingly large sample sizes are necessary to confidently answer the progressively complex biomedical questions the research community is interested in. Automated algorithms have been developed to reduce information-rich 3D MRI images to 1-dimensional summary measures that describe tissue properties and are easy to interpret, such as total gray matter volume. Automated segmentation algorithms save considerable time, compared to manual human inspection, but lack the advanced visual system of humans. As a result, these algorithms often make systematic errors, especially when analyzing brains with pathology or those in the early stages of development. Data science is poised to facilitate complex neuroscience research by fusing a crowdsourcing strategy with machine learning methods; automatic quantification can perform the bulk of the work efficiently and errors can be resolved by non-expert “citizen-scientists” with the advantage of the human visual system. Crowdsourcing has been successful in many other disciplines , including mathematics , astronomy , and biochemistry . Recently, over 200,000 “citizen-neuroscientists” from over 147 countries helped identify neuronal connections in a mouse retina through the Eyewire game . This crowdsourced game led to a new understanding of how mammalian retinal cells detect motion. I propose to implement three key features of the EyeWire paradigm and adapt them for the segmentation of MRI data. First, by breaking up the problem into smaller “micro-tasks”, Eyewire scientists were able to access a much larger user-pool of non-experts. In a similar vein, 3D MRI data can be divided into 2D slices to be segmented by users. Second, machine learning algorithms were trained to help with the task, which improved the speed of manual neuronal tracing and validated non-expert input in the Eyewire game. Deep learning methods have already shown to be successful at segmenting MRI data, and similar models could be built to support manual segmentation. Lastly, EyeWire transformed a dull, monotonous task for experts into a fun, competitive game that trained non-experts and acquired valuable scientific data. The University of Washington is an ideal place to develop a similar game platform for MRI segmentation, using the resources at the Center for Game Science, led by Zoran Popovic. I propose to create an open-source platform for efficiently crowdsourcing brain tissue classification problems in order to answer neuroscience research questions with more precision. Specific Aims 1. SCALEABLE AND SECURE MICRO-TASKS: A scaleable database system and server backend that keeps data private by dividing it into small “micro-tasks” 2. LEARNING BY EXAMPLE: Machine learning algorithm that learns from human curation to improve efficiency of manual tasks 3. TRAINING THROUGH GAMIFICATION: User interface that trains users to solve a specific problem, and keeps them engaged through a reward system